Intercalating agents that bind to double stranded oligonucleotides (e.g., DNA, RNA or hybrids thereof) are well known in the art. In general, intercalating agents are aromatic molecules that non-covalently bind to double stranded oligonucleotides by intercalating themselves between interfacing purine and pyrimidine bases of the two strands of double stranded oligonucleotides. Thus, oligonucleotides carrying, i.e., connected to, an intercalating group can be used in a variety of applications, including as hybridization probes.
Similarly, minor groove binding agents are compounds that bind non-covalently into the minor groove of a double stranded oligonucleotides. However, minor groove binding agents are generally higher molecular weight molecules than intercalating agents. Typically, the molecular weight of minor groove binder agents range from about 150 to about 2000 Daltons. Minor groove binding agents generally bind in a non-intercalating manner into the minor groove of double stranded oligonucleotides. Thus, minor groove binding agents can be used for duplex stabilization and are useful as hybridization improving tools, as well as other applications. For example, hybridization reagents comprising a covalently attached oligonucleotides and minor groove binders are described in U.S. Pat. No. 6,321,894. In addition, using minor groove binders in sequence specific binding and melting temperature modulation have been described in U.S. Pat. Nos. 6,303,312 and 6,221,589, respectively.
Minor groove binder agents usually have a chain of connected (conjugated or non-conjugated) aromatic rings. The presence of a plurality of aromatic rings renders the minor groove binders prone to self-association (aggregation) due to the pi-interaction between the aromatic systems. Aggregation reduces effective concentration of the minor groove binders (poorly soluble) and consequently their minor groove binding performance. One method for reducing non-specific self-associations is to introduce an electrostatic charge within the minor groove binders. Some minor groove binding compounds bearing positive charges at the terminal position of the molecules are known. See, for example, Reddy et al., Pharmacol. Therapeut., 1999, 84, 1-111. The positive charge improves the attraction to the negatively charged DNA duplexes thereby increasing the DNA binding affinity. Unfortunately, however, the positive charge can also increase non-specific binding.
Therefore, there is a need for minor groove binding compounds with reduced self-associations and non-specific binding.